Within the intestinal ecosystem, host tissues, parasites, and populations of gut microbes, collectively called the gut microbiota, are constantly interacting. Each interaction is species-specific, creating unique host-parasite-microbiota systems. We examined the interactions among the host Alouatta caraya (black and gold howler monkey), its gut microbiota, and the zoonotic parasite Giardia intestinalis. Specifically, this study investigated how Giardia infection affects the A. caraya microbiota. We hypothesized that Giardia-positive individuals will have a different and less diverse microbiota structure than Giardia-negative individuals. A. caraya were non-invasively sampled in Corrientes, Argentina, where two fecal samples were collected per individual for pathogen detection and microbiome analysis (n = 65). Molecular analyses were conducted using multi-locus nested amplification and Sanger sequencing for Giardia diagnostics and high throughput microbial 16S rRNA gene sequencing for microbiota characterization. Prevalence of G. intestinalis in A. caraya was 78.5% (51/65), and preliminary data suggest a difference in overall microbiome composition between Giardia positive and negative howlers (PERMANOVA based on Bray-Curtis matrices created in QIIME2, Pseudo-F = 5.28, R2 = 0.03, p-value < 0.001). Howler monkeys rely on gut microbes to buffer against variations in energy availability and nutrient intake over the year, and although they seem to be asymptomatic for Giardia infection, it is possible that the composition and function of their gut microbes are altered during infection, thus impacting their digestion and overall health.